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How to cluster (nearest neighbour method) amino acid peptide sequences based on sequence identity?

Hi,

I have a list of amino-acid peptides. For example:

ILM
FILM
FILVM
..
..

Now I need to cluster (nearest neighbour method) these peptides based on sequence identity

Please suggest any tool to do clustering

Thanks in advance

alignment
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updated by Ram Ram • written by vsivaranjanipriya • vsivaranjanipriya

1 answer

If it is just the matter of sequence identity, uclust/cd-hit would probably be the best. If you want to take into account biochemical properties of amino acids used, there are some more sophisticated tools out there, namely: MUSI and the Gibbs sampling tool (IMHO better than MUSI) and also Hammock (there is also a Galaxy version of it), which is suitable especially for very large datasets.

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updated by Ram Ram • written by jockbanan jockbanan

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